Contacts of the helix formed by residues 527 - 546 (chain C) in PDB entry 5DO7
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 527 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 3.6 26.3 - - + +
443C PRO* 4.0 23.3 - - + -
446C ARG* 4.1 10.8 - - - +
521C LEU* 3.9 16.4 - - + -
525C GLN 3.8 6.7 - - - +
526C ASN* 1.3 87.2 - - - +
528C ASN* 1.3 59.6 + - - +
529C ILE 3.1 0.4 - - - -
530C VAL* 2.8 9.9 + - + +
531C ASN 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 528 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 5.1 1.3 - - - -
526C ASN* 2.5 13.9 + - - +
527C PRO* 1.3 77.1 - - - +
529C ILE* 1.3 50.9 + - - +
531C ASN* 3.5 15.5 + - - +
532C SER* 2.5 34.9 + - - -
556D PHE* 3.8 26.8 - - - -
557D HIS* 3.1 36.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 529 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A ILE* 4.3 25.6 - - + -
524C VAL* 3.9 21.5 - - + -
526C ASN* 2.8 20.3 + - + +
528C ASN* 1.3 74.3 - - - +
530C VAL* 1.3 71.7 + - - +
532C SER* 2.8 22.4 + - - +
533C VAL* 2.8 19.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 530 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 4.7 2.2 - - + -
517C THR* 3.7 33.0 - - + +
520C LEU* 3.8 20.6 - - + -
521C LEU* 3.9 24.7 - - + -
524C VAL* 3.7 29.8 - - + -
526C ASN 4.1 0.4 + - - -
527C PRO* 2.8 16.7 + - + +
529C ILE* 1.3 76.1 - - - +
531C ASN* 1.3 59.4 + - - +
533C VAL* 2.9 9.3 - - - +
534C VAL* 2.8 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 531 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C TYR* 4.1 20.8 + - - -
435C MET* 2.7 44.5 - - - +
436C LEU* 4.9 1.0 - - - +
439C VAL* 4.0 22.2 - - + +
527C PRO 2.8 15.0 + - - +
528C ASN* 3.8 18.9 - - - +
529C ILE 3.1 0.2 - - - -
530C VAL* 1.3 76.0 - - - +
532C SER* 1.3 65.7 + - - +
535C ALA* 3.4 17.8 + - - +
461D PHE* 6.1 0.2 - - - -
465D LEU* 6.2 0.5 - - - +
557D HIS* 5.7 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 532 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528C ASN* 2.5 28.9 + - - -
529C ILE* 2.8 17.9 + - - +
531C ASN* 1.3 76.7 + - - +
533C VAL* 1.3 64.1 + - - +
535C ALA* 3.2 12.1 + - - +
536C LEU* 3.2 13.3 + - - +
461D PHE* 5.0 2.4 - - - -
465D LEU* 4.6 23.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 533 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A PRO* 6.4 1.8 - - + -
561A ILE* 5.2 11.7 - - + -
520C LEU* 3.6 27.8 - - + -
524C VAL* 6.3 0.2 - - + -
529C ILE* 2.8 16.2 + - + +
530C VAL* 2.9 23.3 - - + +
532C SER* 1.3 75.2 - - - +
534C VAL* 1.3 77.0 + - - +
536C LEU* 2.8 20.7 + - + +
537C LEU* 2.8 37.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 534 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C PRO 5.4 0.2 - - - +
435C MET* 3.4 24.7 - - + -
513C GLY* 4.8 6.3 - - - +
516C LEU* 4.1 17.0 - - + -
517C THR* 3.5 28.7 - - - +
520C LEU* 3.9 23.8 - - + -
530C VAL* 2.8 33.6 + - + +
533C VAL* 1.3 72.9 - - - +
535C ALA* 1.3 57.6 + - - +
537C LEU* 3.3 10.5 - - + +
538C SER* 2.8 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 535 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432C TYR* 4.1 14.8 - - + -
435C MET* 3.6 6.6 - - + +
531C ASN* 3.4 11.5 + - - +
532C SER* 3.2 11.4 + - - +
533C VAL 3.0 0.4 - - - -
534C VAL* 1.3 78.3 - - - +
536C LEU* 1.3 65.1 + - - +
538C SER* 2.8 9.6 + - - -
539C ILE* 2.8 30.3 + - + +
461D PHE* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 536 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532C SER 3.2 7.1 + - - +
533C VAL* 2.8 15.9 + - + +
535C ALA* 1.3 75.0 - - - +
537C LEU* 1.3 74.3 + - + +
539C ILE* 4.0 4.3 - - - +
540C ALA* 2.8 35.6 + - + +
427D MET* 4.4 22.9 - - + -
461D PHE* 5.1 11.4 - - + +
462D ASN* 5.4 4.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 537 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C LEU* 3.7 28.0 - - + -
520C LEU* 4.4 8.1 - - + -
533C VAL* 2.8 33.9 + - + +
534C VAL* 3.3 26.2 - - + +
536C LEU* 1.3 87.4 - - + +
538C SER* 1.3 58.4 - - - +
539C ILE 2.9 0.3 + - - -
540C ALA* 3.6 3.6 - - - +
541C GLY* 2.8 30.0 + - - -
568C GLN* 4.2 0.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 538 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428C GLY* 4.0 10.2 + - - -
431C PRO* 3.9 28.1 - - - +
432C TYR* 4.5 7.4 + - - +
435C MET* 4.2 6.4 - - - +
516C LEU* 6.2 1.3 - - - -
534C VAL* 2.8 19.8 + - - -
535C ALA* 2.8 20.0 + - - -
537C LEU* 1.3 73.0 - - - +
539C ILE* 1.3 60.8 + - - +
542C VAL* 3.9 10.4 - - - +
567C PHE* 4.9 3.4 - - - -
568C GLN* 3.4 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 539 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C TYR* 5.6 2.2 - - - +
428C GLY* 4.1 15.0 - - - +
432C TYR* 4.7 18.2 - - + -
535C ALA* 2.8 23.6 + - + +
536C LEU* 4.0 4.0 - - - +
538C SER* 1.3 82.4 - - - +
540C ALA* 1.3 71.3 + - - +
541C GLY 3.1 0.7 - - - -
542C VAL* 2.8 31.0 + - + +
543C LEU* 3.4 5.7 + - + +
458D LEU* 6.1 5.8 - - + -
461D PHE* 4.9 21.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 540 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536C LEU* 2.8 30.0 + - + +
537C LEU* 3.6 3.8 - - - +
539C ILE* 1.3 74.5 - - - +
541C GLY* 1.3 66.8 + - - +
543C LEU* 2.8 27.0 + - - +
544C VAL* 3.4 10.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 541 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537C LEU 2.8 13.0 + - - -
540C ALA* 1.3 76.9 - - - +
542C VAL* 1.3 57.5 + - - +
544C VAL* 3.2 9.3 - - - +
545C GLY* 2.8 28.9 + - - -
566C THR* 4.5 6.6 - - - +
568C GLN* 3.2 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 542 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C TYR* 3.1 37.3 - - + +
427C VAL* 3.6 10.3 - - + +
428C GLY* 3.4 36.8 - - - +
538C SER 3.9 4.0 - - - +
539C ILE* 2.8 36.7 + - + +
541C GLY* 1.3 71.1 - - - -
543C LEU* 1.3 56.2 + - - -
546C SER* 2.2 45.5 + - - +
568C GLN* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 543 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C TYR* 3.7 17.3 - - - +
539C ILE* 4.3 4.9 - - + +
540C ALA* 2.8 20.6 + - - +
542C VAL* 1.3 79.0 - - - +
544C VAL* 1.3 61.1 + - + +
546C SER 4.4 1.4 + - - -
547C GLY 4.7 1.9 + - - +
549C LEU* 4.3 23.6 + - + +
550C ARG* 4.7 7.3 + - + +
555C MET* 5.0 0.2 - - - +
431D ILE* 5.8 4.9 - - + -
434D LEU* 3.6 34.8 - - + -
435D TYR* 4.2 13.7 - - + +
454D MET* 4.0 31.6 - - + -
458D LEU* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 544 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540C ALA* 3.5 10.3 - - + +
541C GLY* 3.2 18.8 - - - +
543C LEU* 1.3 81.4 - - + +
545C GLY* 1.3 61.7 + - - +
546C SER 3.4 0.7 + - - -
547C GLY 4.1 5.4 + - - -
552C ILE* 4.5 2.9 - - - +
555C MET* 3.5 24.8 - - + +
559C PHE* 4.1 23.1 - - + -
562C ILE* 4.6 17.9 - - + -
563C SER* 3.7 16.7 - - - +
566C THR* 4.8 4.3 - - + -
434D LEU* 3.2 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 545 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541C GLY 2.8 20.5 + - - -
544C VAL* 1.3 72.4 - - - +
546C SER* 1.3 60.8 + - - +
547C GLY 3.4 0.7 - - - -
552C ILE* 5.2 0.8 - - - +
563C SER* 4.0 11.2 - - - -
566C THR* 3.8 18.4 - - - -
568C GLN 4.3 0.2 - - - -
569C LYS* 2.5 41.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 546 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C TYR* 4.0 4.2 - - - -
427C VAL* 4.5 0.9 - - - +
542C VAL* 2.2 44.3 + - - +
543C LEU 5.0 0.4 - - - -
545C GLY* 1.3 80.5 - - - +
547C GLY* 1.3 58.1 + - - +
548C PHE* 3.1 41.5 + - - -
549C LEU 5.4 0.2 - - - -
552C ILE* 5.4 0.7 - - - -
568C GLN* 4.7 0.9 - - - +
569C LYS 4.7 0.4 - - - +
572C SER* 3.7 24.4 + - - -
573C GLU* 4.5 13.0 - - - +
612C THR* 5.7 0.3 - - - -
613C CYS* 5.0 5.0 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il